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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada ↵4 Present address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Corresponding author: gsmith@fredhutch.orgAbstractMany phages encode recombination-mediating enzymes...
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Method: Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption
- Meir Goldenberg,
- Loay Mualem,
- Amit Shahar,
- Sagi Snir,
- and Adi Akavia
Genome Res. September 2024 34: 1324-1333; Published in Advance September 5, 2024, doi:10.1101/gr.279071.124
...the sensitivity of this data, it is essential to safeguard both inputs and outputs of the EPM model. A privacy-preserving approach for EPM computation utilizing fully homomorphic encryption was recently introduced. However, this method has limitations, including having high communication complexity and being...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several s of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme scrambling caused by thousands of chromosomal rearrangements, although showing...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...).Chromosome fusions involving X/Z often synchronously generate sex-limited chromosomes, neo-Y/W, that degenerate through the suppression of recombination. Hemizygosity of genes linked to the neo-X/Z Chromosome then selects for dosage compensation (Natri et al. 2013; Sigeman et al. 2021). This process occurs...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...: It is essential for correct disjunction of chromosomes during cell division, and it generates new combinations of genetic variants that form the raw material of evolution (Hartfield and Keightley 2012). However, recombination can also be deleterious, as it can generate structural mutations and break up favorable...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...-read sequencing cannot resolve the complex segmental duplications (SDs) to provide direct confirmation of the hypothesis that the rearrangements are caused by nonallelic homologous recombination between the low copy repeats on Chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...to close most of the repetitive gaps and achieved 99.9% completeness (Miga et al. 2020; Logsdon et al. 2021; Hoyt et al. 2022; Nurk et al. 2022; Rautiainen et al. 2023). In particular, the method developed to assemble human Chromosome 8 depended on the use of single-copy k-mers (hereafter called unikmers...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...De novo assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of reshuffling and uncover novel 3D folding in amniotes Basanta Bista1,7, Laura González-Rodelas2,3,7, Lucía Álvarez-González2, Zhi-qiang Wu1,4, Eugenia E. Montiel1,8, Ling Sze Lee1...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...a spearheading attempt to describe the fine-scale variation in recombination rate in a butterfly. The wood white is widely distributed across western Eurasia and shows extreme variation in chromosome numbers, with a cline-like pattern increasing from 2n∼56–60 in the northern (Scandinavia) and eastern (central...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...mutations and facilitating their independent fixation or loss (Webster and Hurst 2012). However, in contrast to mutation rates, recombination rates have frequently been estimated in mapping studies. These have shown that recombination rates vary within and between chromosomes, individuals, sexes...
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